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Common sense would give you an answer in two and a bit words: He can't.

But this is a manga and it's the title characters fight, he ain't loosing/dying. Anything could happen but in the end the Leaf will have avoided destruction and most/all main characters will be alive. Gods puppets will somehow have died(somehow but probably not all) but his original will still be somewhere.

Pein has 6 body + he has Konan with him. he isn't alone. Anyhow, if he make Pain rethreat somehow, it's like asking how did Sasuke "capture" Hachibi lol. Total non sense but that's why naruto is all about since shipuden.

its funny how some people underestimate both the leaf village and pain himself..... dont forget pain has destroyed a whole village all by himself and the leaf village is the one of strongest villages if it isnt the strongest.... also naruto has something under his sleeves which will help him againt pain, but i dont think pain will lose the battle or even lose one of his bodies.. i think he is going to retreat after finding out that sasuke fucked up with the 8 tails beast, cuz u know they have to catch them in order

Nop, I prefer Naruto to pain/Sasuke but the strengh gap between the 2 is too much. If Naruto could have a grasp and team with kyuubi then yes , now that would be a awesome epic fight, but would that happen? Nop. So Impossible for Naruto, specialy that what 1-2week of training and grasping he sage mode, couple day to learn frog kata or whatever, you expect him to be strong enough to fight a god? lol...

If I had to guess, Naruto will get back to fight God-Pain, while at the same time the other jounin will finish off the other Pain bodies. Then Shizune's revelation that the bodies were being controlled by chakra waves projected from some area will make them realize fully what Jiraiya meant, and they'll start searching for the person behind Pain. Konan herself may even be captured and interrogated to help reveal the information.

At some point there will be a battle with the real Pain, and that will be the end of this arc. Then Madara is left as the main villain, since he's the last person who's still trying to create a new Ninja World War, which will make him Naruto's final opposition to creating a new better world, like the prophecy predicts.

Konoha (Tsunade) is trusting on Naruto to take care of Pain when he will attack Konoha.

Personally, I think this is absurd!
Pain, a Ninja who has never lost and beat many great Ninjas such as Jiraya and Hanzo, cannot lose to Naruto who did few days of Sage training and now has (more or less) The same Sage abilities like Jiraya did.
I am not gonna put aside The fact that Jiraya was much better than Naruto in other fields if not ALL The other fields.

I really liked The clone training concept. a good explanation how Naruto can get real strong in a short time.
But this doesn't work here.

Also, Konoha didn't learn any thing about Pain - which could help Naruto.

At The moment I don't see how can Naruto win.

naruto is the destiny child that's why everybody have fate on him.
he gonna take pein down no matter what.